US10301683B2 - RNA-biomarkers for diagnosis of prostate cancer - Google Patents

RNA-biomarkers for diagnosis of prostate cancer Download PDF

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US10301683B2
US10301683B2 US15/101,150 US201415101150A US10301683B2 US 10301683 B2 US10301683 B2 US 10301683B2 US 201415101150 A US201415101150 A US 201415101150A US 10301683 B2 US10301683 B2 US 10301683B2
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seq
sample
prostate cancer
prostate
samples
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US20160304967A1 (en
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Friedemann Horn
Jörg Hackermüller
Sabina Christ
Kristin Reiche
Manfred Wirth
Michael Fröhner
Susanne Füssel
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Fraunhofer Gesellschaft zur Forderung der Angewandten Forschung eV
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention is in the field of biology and chemistry.
  • the invention is in the field of molecular biology. More particularly, the invention relates to the analysis of RNA transcripts. Most particularly, the invention is in the field of diagnosing prostate cancer.
  • Prostate cancer is the most frequently diagnosed cancer in men. In 2012, the annual number of newly diagnosed prostate cancer cases was reported as approximately 240,000 cases in the United States and approximately 360,000 in the European Union, 68,000 of which in Germany. In the United States, lifetime risks for prostate cancer diagnosis and for dying of prostate cancer are currently estimated at 15.9% and 2.8%, respectively. Despite widespread screening for prostate cancer and major advances in the treatment of metastatic disease, prostate cancer remains the second most common cause of cancer death for men with over 250,000 deaths each year in the Western world.
  • PSA prostate-specific antigen
  • RNA biomarkers which had not so far been found to be suitable for use in the diagnosis of prostate cancer.
  • the invention relates to a method for the diagnosis of prostate cancer comprising the steps of analysing the expression level of a nucleic acid selected from the group of SEQ ID NO: 1 to 42, wherein, if at least one of said nucleic acids is present and/or the expression level of at least one of said nucleic acids is above a threshold value, the sample is designated as prostate cancer positive.
  • the invention relates to a method for the diagnosis of prostate cancer comprising the steps of analysing in a sample from a patient the expression level of a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, wherein, if the expression level of said nucleic acid is above a threshold value, the sample is designated as prostate cancer positive.
  • the invention relates to a primer or probe that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, or any part thereof.
  • the invention also relates to the use of a primer or probe that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29 for the diagnosis of prostate cancer.
  • the invention relates to a probe or primer, wherein the probe or primer is specific for a sequence of the group of SEQ ID NO: 1 to 42, preferably for a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29.
  • the invention relates to a nucleic acid with a sequence from the group of SEQ ID NO: 1 to 42, or the reverse complement thereof, or a nucleic acid that shares preferably at least 85%, 90%, 95% or 99% sequence identity with a nucleic acid according to any one of the nucleic acids according to SEQ ID NO: 1 to 42.
  • the invention relates to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, or the reverse complement thereof, or a nucleic acid that shares preferably at least 85%, 90%, 95% or 99% sequence identity with the selected nucleic acid.
  • the invention relates to the use of a nucleic acid with a sequence from the group of SEQ ID NO: 1 to 42 for the diagnosis of prostate cancer.
  • the invention relates to the use of a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, for the diagnosis of cancer.
  • the invention also relates to a kit for the diagnosis of prostate cancer comprising a nucleic acid that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, and reagents for nucleic acid amplification and/or quantification and/or detection.
  • a kit for the diagnosis of prostate cancer comprising a nucleic acid that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, and reagents for nucleic acid amplification and/or quantification and/or detection.
  • FIG. 1 Verification of tissue sample quality: to determine the tumour cell content of the tissue samples, cryosections were prepared from the frozen samples as shown.
  • HE hematoxylin/eosin
  • IHC immunohistochemistry.
  • Verification of tissue sample quality cryosections of 4J.-Lm were prepared from the frozen samples as shown for HE staining (to ensure tumour cell content of the tissue samples), for RNA and DNA isolation and for IHC.
  • HE hematoxylin/eosin
  • IHC immunohistochemistry.
  • FIG. 2 Box plot of RNA-seq data for transcript PCA3.
  • FIG. 3 ROC curves of Retro-RPL7 (SEQ ID NO 1) and PCA3 obtained by qRT-PCR analysis of 56 prostate tissue samples.
  • FIG. 4 RNA Next-Generation Sequencing data for SEQ ID NO: 26 to 29 from 64 tissue samples.
  • 8 control tissue samples originated from patients with benign prostate hyperplasia (BPH) and 56 tissue samples were obtained from patients with prostate cancer upon radical prostatectomy (RPE). Amongst the latter, 40 samples represented tumour tissue containing a tumour cell count of at least 60% whereas 16 samples represented adjacent tumour-free tissue (tumour cell count of max. 5%) derived from the same patients.
  • A Box plot showing the normalised counts for the nucleic acid with SEQ ID NO: 26 to 29.
  • B ROC curve of the comparison of nucleic acid with SEQ ID NO: 26 to 29 expression levels between tumour and control samples: Area under the ROC curve (AUC): 0.9438.
  • FIG. 5 Custom microarray data for SEQ ID NO: 12 from 256 tissue samples.
  • 40 control tissue samples originated from patients with benign prostate hyperplasia (BPH) and 216 tissue samples were obtained from patients with prostate cancer upon radical WO 2015/082417 PCT/EP2014/07614332 prostatectomy (RPE). Amongst the latter, 164 samples represented tumour tissue whereas 52 samples represented adjacent tumour-free tissue derived from the same patients.
  • RPE radical WO 2015/082417 PCT/EP2014/07614332 prostatectomy
  • 164 samples represented tumour tissue whereas 52 samples represented adjacent tumour-free tissue derived from the same patients.
  • A Box plot showing the normalised counts for the nucleic acid with SEQ ID NO: 12.
  • B ROC curve of the comparison of nucleic acid with SEQ ID NO: 12 expression levels between tumour and control samples: Area under the ROC curve (AUC): 0.8485.
  • FIG. 6 Urine samples of patients with prostate cancer (Tumour) and healthy patients (Control) were obtained after digital rectal examination by a urologist. RNA isolated from these samples was subjected to transcriptome-wide RNA sequencing using an Illumina HiSeq2500 next-generation sequencer. Reads were mapped to the genome by standard algorithms. Reads mapping to the genomic loci of the transcript SEQ ID NOs shown were counted and normalized to reads derived from the gene locus of prostate-specific antigen as a measure for the presence of prostate epithelium cells in the urine for normalisation. Read numbers (million) are shown as log 2 values.
  • nucleic acid(s) or “nucleic acid molecule” generally refers to any ribonucleic acid or deoxyribonucleic acid, which may be unmodified or modified.
  • Nucleic acids include, without limitation, single- and double-stranded nucleic acids.
  • nucleic acid(s) also includes nucleic acids as described above that contain one or more modified bases. Thus, a nucleic acid with one or several backbone modifications for stability or for other reasons is a “nucleic acid”.
  • nucleic acids encompasses such chemically, enzymatically or metabolically modified forms of nucleic acids, as well as the chemical forms of nucleic acids characteristic of viruses and cells, including for example, simple and complex cells.
  • level or “expression level” in the context of the present invention relate to the level at which a biomarker is present in a sample from a patient.
  • the expression level of a biomarker is generally measured by comparing its expression level to the expression level of one or several housekeeping genes in a sample for normalisation.
  • the sample from the patient is designated as prostate cancer positive if the expression level of the biomarker exceeds the expression level of the same biomarker in an appropriate control (for example a healthy tissue) by a set threshold value.
  • RNA can also be analysed for example by northern blot, next generation sequencing or after amplification by using spectrometric techniques that include measuring the absorbance at 260 and 280 nm.
  • the term “amplified”, when applied to a nucleic acid sequence, refers to a process whereby one or more copies of a particular nucleic acid sequence is generated from a nucleic acid template sequence, preferably by the method of polymerase chain reaction.
  • Other methods of amplification include, but are not limited to, ligase chain reaction (LCR), polynucleotide-specific based amplification (NSBA), or any other method known in the art.
  • correlating refers to comparing the presence or amount of the marker(s) in a sample from a patient to its presence or expression level in a sample from a person known to suffer from, or is at risk of suffering from, a given condition.
  • a marker expression level in a patient sample can be compared to a level known to be associated with a specific diagnosis.
  • diagnosis refers to the identification of the disease, in this case prostate cancer, at any stage of its development, and also includes the determination of predisposition of a subject to develop the disease.
  • Ensembl gene ID ENSG00000255545.3 relates to a gene ID sequence annotation by Ensembl. Transcripts that belong to the same gene ID may differ in splice events, exons, and can give rise to very different proteins. These are isoforms, arising from alternative splicing.
  • the Ensembl gene ID has several equivalents in other annotation systems such as for example RP11-627G23.1, or locus (hg19) Chr11: 134,306,367-134,375,555 (+). Any equivalent to this Ensembl annotation can be used in its place.
  • splice variant refers to the product of an alternative splicing event.
  • Alternative splicing events include exon skipping or inclusion, alternative 5′ or 3′ splice site usage, or intron retention.
  • fluorescent dye refers to any chemical that absorbs light energy of a specific wavelength and re-emits light at a different wavelength.
  • Fluorescent dyes suitable for labelling nucleic acids include for example FAM (5- or 6-carboxyfluorescein), VIC, NED, Fluorescein, FITC, IRD-700/800, CY3, CY5, CY3.5, CY5.5, HEX, TET, TAMRA, JOE, ROX, BODIPY TMR, Oregon Green, Rhodamine Green, Rhodamine Red, Texas Red, Yakima Yellow, Alexa Fluor, PET and the like.
  • isolated when used in reference to a nucleic acid means that a naturally occurring sequence has been removed from its normal cellular (e.g. chromosomal) environment or is synthesised in a non-natural environment (e.g. artificially synthesised). Thus, an “isolated” sequence may be in a cell-free solution or placed in a different cellular environment.
  • kits are packaged combinations optionally including instructions for use of the combination and/or other reactions and components for such use. If the kit contains nucleic acids, the kit may also comprise synthetic or non-natural variants of said nucleic acids.
  • a synthetic or non-natural nucleic acid is to be understood as a nucleic acid comprising any chemical, biochemical or biological modification, such that the nucleic acid does not appear in nature in this form. Such modifications include, but are not limited to, labelling with a fluorescent dye or a quencher moiety, a biotin tag, as well as modification(s) in the backbone of a nucleic acid, or any other modification that distinguishes the nucleic acid from its natural counterpart. The same applies also to other natural compounds such as proteins, lipids and the like.
  • patient refers to a living human or non-human organism that is receiving medical care or that should receive medical care due to a disease, or is suspected of having a disease. This includes persons with no defined illness who are being investigated for signs of pathology. Thus the methods and assays described herein are applicable to both, human and veterinary disease.
  • primer refers to an nucleic acid, whether occurring naturally as in a purified restriction digest or produced synthetically, which is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid strand, is induced, i.e., in the presence of nucleotides and an inducing agent such as a DNA polymerase and at a suitable temperature and pH.
  • the primer may be either single-stranded or double-stranded and must be sufficiently long to prime the synthesis of the desired extension product in the presence of the inducing agent. The exact length of the primer will depend upon many factors, including temperature, source of primer and the method used.
  • primers have a length of from about 15-100 bases, more preferably about 20-50, most preferably about 20-40 bases.
  • the primer can be a synthetic element, in the sense that it comprises a chemical, biochemical or biological modification.
  • modifications include, but are not limited to, labelling with a fluorescent dye or a quencher moiety, or a modification in the backbone of a nucleic acid, or any other modification that distinguishes the primer from its natural nucleic acid counterpart.
  • probe refers to any element that can be used to specifically detect a biological entity, such as a nucleic acid, a protein or a lipid. Besides the portion of the probe that allows it to specifically bind to the biological entity, the probe also comprises at least one modification that allows its detection in an assay. Such modifications include, but are not limited to labels such as fluorescent dyes, a specifically introduced radioactive element, or a biotin tag. The probe can also comprise a modification in its structure, such as a locked nucleic acid.
  • sample refers to a sample of bodily fluid or tissue obtained for the purpose of diagnosis, prognosis, or evaluation of a subject of interest, such as a patient.
  • Preferred test samples include blood, serum, plasma, cerebrospinal fluid, urine, saliva, sputum, and pleural effusions.
  • a fractionation or purification procedure for example, separation of whole blood into serum or plasma components.
  • the sample is selected from the group comprising a blood sample, a serum sample, a plasma sample, a cerebrospinal fluid sample, a saliva sample and a urine sample or an extract of any of the aforementioned samples as well as circulating tumour cells in blood or lymph, any tissue suspected to contain metastases as well as any source that may contain prostate tumour cells or parts thereof, including vesicles like exosomes, microvesicles, and others as well as free or protein-bound RNA molecules derived from prostate tumour cells.
  • the sample is a blood sample, most preferably a serum sample or a plasma sample.
  • urine (particularly after digital rectal examination) and ejaculate belong to the most preferable samples.
  • Tissue samples may also be biopsy material or tissue samples obtained during surgery.
  • AUC area under the curve
  • ROC receiver operating characteristic
  • p-value relate to the probability of obtaining the observed sample results (or a more extreme result) when the null hypothesis is actually true, i.e. there are no differences between means for groups. The smaller the p-value, the higher the likelihood that the alternative hypothesis explains the observed results better than the null hypothesis.
  • adjusted p-value refers to p-values which have been adjusted for multiple comparisons (number of genes/probes tested). The method applied is detailed in the experimental section.
  • the invention describes a method of diagnosis of prostate cancer.
  • This method comprises analysing a sample taken from a patient and specifically determining the level of a biomarker or a combination of biomarkers in said patient sample. The result is then correlated to a threshold value and in the case where it is above that threshold value, said patient sample is designated as prostate cancer positive.
  • the invention relates to a group of sequences comprising SEQ ID NOs 1 to 42.
  • the sequences are listed below. Due to space constraints, only the first 100 nucleotides are listed. The remaining part of the sequence can be found in the sequence protocol.
  • transcripts are known sequences that are already annotated in relevant databases. They are identified by their respective annotations.
  • new transcripts were identified that are not yet annotated. They are designated here as follows: XLOC followed by a number. These designations provide information about the genomic origins of the transcripts, but may not necessarily represent the whole sequence of a given transcript. The sequences as detected may in some cases be longer or shorter. In the case of XLOC transcripts, if fragments are detected, these fragments may be as small as 1000, 500, 400, 300, 200, 150, 100, 50, 40, 30, 20, 10, 9, 8, 7, 6 or 5 nucleotides.
  • PCA3 prostate carcinoma
  • Retro-RPL7 SEQ ID NO: 1
  • AUC area under the ROC curve
  • the area under the ROC curve for this biomarker in the sequencing experiment is 0.944.
  • the differential expression of SEQ ID NOs: 26 to 29 could be validated by custom array analysis of 256 tissue samples ( FIG. 5 ).
  • the invention relates to a method for the diagnosis of prostate cancer comprising the steps of analysing the expression level of the nucleic acid according to SEQ ID NO: 1 to 42, wherein, if at least one of said nucleic acids is present and/or the expression level of at least one of said nucleic acids is above a threshold value, the sample is designated as prostate cancer positive.
  • the invention relates to a method for the diagnosis of prostate cancer comprising the steps of analysing in a sample from a patient the expression level of a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, wherein, if the expression level of said nucleic acid is above a threshold value, the sample is designated as prostate cancer positive.
  • the invention relates to a method for the diagnosis of prostate cancer comprising the steps of analysing in a sample from a patient the expression level of a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group consisting of SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, wherein, if the expression level of said nucleic acid is above a threshold value, the sample is designated as prostate cancer positive.
  • analysing the expression level of a nucleic acid means analysing the reverse complement or the cDNA of the nucleic acid.
  • the sample is selected from the group comprising prostate tissue, biopsy material, lymph nodes, urine, ejaculate, blood, blood serum, blood plasma, circulating tumour cells in blood or lymph, any tissue suspected of containing metastases as well as any source that may contain prostate tumour cells or parts thereof, including vesicles like exosomes, micro vesicles, and others as well as free or protein-bound RNA molecules derived from prostate tumour cells or parts thereof. More preferably, the sample is urine, and most preferably, the sample is urine obtained from a patient after a digital rectal examination.
  • the expression level of a transcript of the nucleic acids according to SEQ ID NO: 1 to 42 is compared to the expression level of one or several other gene transcripts in the sample, such as of housekeeping genes. Examples of suitable housekeeping genes are shown below in Table 2:
  • the threshold value is the minimal expression difference between the test sample and the control sample at which the sample is designated as cancer-positive.
  • the threshold value for the biomarker expression level difference between the test sample and the control sample is 1.5 fold ( ⁇ 20%), 2 fold ( ⁇ 20%), 3 fold ( ⁇ 20%), 4 fold ( ⁇ 20%) and most preferably 5 fold ( ⁇ 20%) or more.
  • the p-value (T test) is ⁇ 2 ⁇ 10 ⁇ 5 .
  • the FDR is preferably ⁇ 5 ⁇ 10 ⁇ 4 .
  • the threshold is preferably a 2 fold expression level increase between the test sample and the control sample to designate a sample as prostate cancer positive.
  • the invention is concerned with the quantification of the expression level of RNA biomarkers. After amplification, quantification is straightforward and can be accomplished by a number of methods. In the case when primers are used wherein at least one primer has a fluorescent dye attached, quantification is possible using the fluorescent signal from the dye.
  • Various primer systems and dyes are available, such as SYBR green, Multiplex probes, TaqMan probes, molecular beacons and Scorpion primers. These are suitable for instance to carry out PCR-based methods such as quantitative reverse transcription PCR (qRT-PCR).
  • Other possible means of quantification are for example northern blotting, next generation sequencing or absorbance measurements at 260 and 280 nm.
  • any suitable method for the quantification of nucleic acids may be used to analyse the expression levels of the nucleic acids.
  • the analysis in the method is performed by a fluorescence based assay.
  • the analysis is done by measuring the fluorescence of a labelled primer, labelled probe or a fluorescent detection agent (such as SYBR green). More preferably, this analysis of the expression level is performed by qRT-PCR.
  • the sample is mixed with a forward and a reverse primer specific for at least one nucleic acid selected from the group of SEQ ID NO: 1 to 42, preferably a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, followed by amplification.
  • Probes or primers are designed such that they hybridize under stringent conditions to said target sequence.
  • the analysis of the expression level is performed by next generation sequencing.
  • the protein product of one of SEQ ID NO: 1 to 42 is analysed and/or quantified.
  • the invention also relates to a primer or probe that hybridizes under stringent conditions to one of the nucleic acids according to SEQ ID NO: 1 to 42.
  • the invention relates to a primer or probe that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, or any part thereof, wherein said primer or a probe is preferably a labelled probe.
  • the primer or probe that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, is about 5 to 500 nt in length, more preferably, 10 to 200 nt, even more preferably 10 to 100 nt.
  • said nucleic acid is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nt in length.
  • the primer or probe that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, comprises a detectable label.
  • the primer or probe that hybridizes and stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29 additionally comprises a quencher moiety.
  • the invention also relates to the use of a primer or probe that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29 for the diagnosis of prostate cancer.
  • the invention relates to a primer or probe that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group consisting of SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, or any part thereof, wherein said primer or a probe is preferably a labelled probe.
  • the invention further relates to a nucleic acid with a sequence from the group of SEQ ID NO: 1 to 42, or the reverse complement thereof, or a nucleic acid that shares preferably at least 85%, 90%, 95% or 99% sequence identity with a nucleic acid according to any one of the nucleic acids according to SEQ ID NO: 1 to 42.
  • the invention relates to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29 or the reverse complement thereof, or a nucleic acid that shares preferably at least 85%, 90%, 95% or 99% sequence identity with the selected nucleic acid.
  • the invention relates to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group consisting of SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29 or the reverse complement thereof, or a nucleic acid that shares preferably at least 85%, 90%, 95% or 99% sequence identity with the selected nucleic acid.
  • the invention further relates to the use of a nucleic acid with a sequence from the group of SEQ ID NO: 1 to 42 for the diagnosis of prostate cancer.
  • the invention relates to the use of a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, or its revers complement for the diagnosis of cancer.
  • the invention relates to the use of a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group consisting of SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, or its revers complement for the diagnosis of cancer.
  • the invention also relates to a kit for the screening and/or diagnosis of prostate cancer comprising a probe or primer that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29.
  • the kit may contain more than one nucleic acid.
  • the kit additionally comprises reagents for nucleic acid amplification and/or quantification and/or detection.
  • the kit comprises control samples.
  • the invention also relates to a kit for the screening and/or diagnosis of prostate cancer comprising a probe or primer that hybridizes under stringent conditions to a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group consisting of SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29.
  • the kit may contain more than one nucleic acid.
  • the kit additionally comprises reagents for nucleic acid amplification and/or quantification and/or detection.
  • the kit comprises control samples.
  • the invention relates to a method for the treatment and diagnosis of prostate cancer comprising the steps of analysing in a sample from a patient the expression level of a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, wherein, if the expression level of said nucleic acid is above a threshold value, the sample is designated as prostate cancer positive; and administering to the patient one or more Prostate Cancer Therapeutic Agents.
  • a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group comprising SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, wherein, if the expression level of said nucleic acid is above a threshold value, the sample is designated as prostate cancer positive; and administering to the patient one or more Prostate Cancer Therapeutic Agents.
  • the invention relates to a method for the treatment and diagnosis of prostate cancer comprising the steps of analysing in a sample from a patient the expression level of a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group consisting of SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, wherein, if the expression level of said nucleic acid is above a threshold value, the sample is designated as prostate cancer positive; and administering to the patient one or more Prostate Cancer Therapeutic Agents.
  • a splice variant of Ensembl gene ID ENSG00000255545.3 selected from the group consisting of SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, and SEQ ID NO: 29, wherein, if the expression level of said nucleic acid is above a threshold value, the sample is designated as prostate cancer positive; and administering to the patient one or more Prostate Cancer Therapeutic Agents.
  • the Prostate Cancer Therapeutic Agents comprises: Docetaxel (Taxotere®); Cabazitaxel (Jevtana®); Mitoxantrone (Novantrone®); Estramustine (Emcyt®); Doxorubicin (Adriamycin®); Etoposide (VP-16); Vinblastine (Velban®); Paclitaxel (Taxol®); Carboplatin (Paraplatin®); Abiraterone acetate, Bicalutamide, Casodex, Degarelix, Enzalutamide, Goserelin acetate, Leuprolide acetate, Prednisone, Sipuleucel-T, Radium 223 dichloride and/or Vinorelbine (Navelbine®).
  • the invention discloses biomarkers for prostate cancer, which allow a more accurate and sensitive diagnosis of the disease than current biomarkers.
  • PCa Prostate carcinoma (PCa) patients who underwent radical prostatectomy (RPE) or surgery to remove a benign prostate hyperplasia (BPH) at the University Hospital of Dresden were included in a retrospective clinical cohort aiming at identifying novel biomarkers for PCa. Approval from the local ethics committee as well as informed consent from the patients were obtained according to the legal regulations. Data on the clinical follow-up were collected for at least five years for the PCa patients.
  • RPE radical prostatectomy
  • BPH benign prostate hyperplasia
  • Prostate tissue samples from a cohort of 40 PCa patients and 8 BPH patients were used for identification of diagnostically relevant biomarkers by genome-wide RNA sequencing.
  • PCa groups were defined based on staging according to Gleason (The Veteran's Administration Cooperative Urologic Research Group: histologic grading and clinical staging of prostatic carcinoma; in Tannenbaum, M. Urologic Pathology: The Prostate, Philadelphia: Lea and Febiger. Pp. 171-198) as well as the presence of metastases in the adjacent lymph nodes upon RPE (see Table 3).
  • the control group (C) consists of BPH samples.
  • Selected biomarker candidates were further validated by custom microarrays and quantitative reverse-transcription real-time PCR (qRT-PCR) on cohorts comprising 256 (40 control BPH, 216 tumour samples) and 56 patients (16 control BPH samples, 40 tumour samples), respectively.
  • qRT-PCR quantitative reverse-transcription real-time PCR
  • Prostate tissue samples were obtained from surgery carried out at the Dept. of Urology of the University Hospital of Dresden and stored in liquid nitrogen at the Comprehensive Cancer Centre of Dresden University.
  • Prostate tissue samples obtained from radical prostatectomies (RPEs) of prostate carcinoma (PCa) patients were divided into tumour and tumour-free samples.
  • Prostate tissue samples from patients with benign prostate hyperplasia (BPH) were used as controls. Patient consent was always given.
  • cryosections were prepared using a cryomicrotome (Leica) equipped with a microtome blade C35 (FEATHER) cooled to ⁇ 28° C. Every sample was cut into a total of 208 cryosections, 4 of which were HE-stained and evaluated by a pathologist with respect to their tumour cell content ( FIG. 1 ). This yielded 3 stacks of consecutive cryosections, each of which was flanked by HE-stained sections. Only stacks that were flanked on either side by sections containing at least 60% or at most 5% tumour cells were used as tumour or tumour-free samples, respectively. 50 cryosections of the stacks chosen were then subjected to RNA preparation.
  • Agilent Bioanalyzer 2100 Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, Calif.), and only RNA samples with an RNA-Integrity-Number (RIN) of at least 6 were further processed.
  • RNA sequencing was performed using a subset of the retrospective PCa cohort comprising 8 prostate tissue samples from benign prostate hyperplasia (BPH) as a control and 56 samples from patients with prostate cancer (including tumour and tumour-free tissue pairs from samples with Gleason score >7).
  • 1 ⁇ g of total RNA was depleted of ribosomal RNA using the Ribo-Zero rRNA Removal Kit (Epicentre).
  • Sequencing libraries were prepared from 50 ng of rRNA-depleted RNA using ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre).
  • the di-tagged cDNA was purified using the Agencourt AMPure XP System Kit (Beckman Coulter).
  • PCR was carried out through 10 cycles to incorporate index barcodes for sample multiplexing and amplify the cDNA libraries.
  • the quality and concentration of the amplified libraries were determined using a DNA High Sensitivity Kit on an Agilent Bioanalyzer (Agilent Technologies). 4 ng each of 8 samples were pooled and size-selected on 2% agarose gels using agarose gel electrophoresis. The sample range between 150 bp and 600 bp was gel-excised and purified with the MinElute Gel Extraction Kit (Qiagen), according to manufacturer's instructions. The purified libraries were quantified on an Agilent Bioanalyzer using a DNA High Sensitivity Chip (Agilent Technologies).
  • Raw sequencing data comprising base call files (BCL files) was processed with CASA VA v1.8.1 (Illumina) resulting in FASTQ files.
  • FASTQ files contain for each clinical sample all sequenced RNA fragments, in the following referred to as “reads”. Specific adapter sequences were removed by using cutadapt (code.google.com/p/cutadapt/). The listing of claims set forth below will replace all prior versions and listings of claims in the application.
  • Htseq-count v0.5.4p1 huber.embl.de/users/anders/HTSeq/doc/count.html
  • Htseq-count v0.5.4p1 huber.embl.de/users/anders/HTSeq/doc/count.html
  • Differentially expressed transcripts and genes were identified using R and the Bioconductor libraries edgeR.
  • Different RNA composition of the clinical samples was adjusted for by scaling library size for each sample (TMM method).
  • TMM method negative binomial log-linear model was fitted to the read counts for each transcript or gene, and coefficients distinct from zero identified by a likelihood ratio test. False discovery rate was controlled by Benjanimi-Hochberg adjustment.
  • the microarray screening was performed using the retrospective PCa cohort comprising 40 prostate tissue samples from patients with benign prostate hyperplasia (BPH) as a control as well as 164 and 52 tumour and tumour-free tissue samples, respectively, of prostate cancer patients after radical prostatectomy.
  • BPH benign prostate hyperplasia
  • cRNA Quick Amp Labeling Kit
  • a probe must exhibit a nonspecific change of expression of at least IQR greater than 0.5.
  • a linear model was fitted using the R package limma and reliable variance estimates were obtained by Empirical Bayes moderated t-statistics. False discovery rate was controlled by Benjamini-Hochberg adjustment.
  • cDNA was synthesized from 100 ng total RNA using the High-Capacity Reverse transcription kit (Applied Biosystems) and random primers according to manufacturer's instructions. Subsequent PCR assays were run using 4 ⁇ l of the diluted cDNA. Quantitative real-time PCR was performed using custom- and pre-designed TaqMan Gene Expression Assays (Applied Biosystems) for housekeeping and target transcripts on an Applied Biosystems 7900HT Real-Time PCR System.
  • ROC Receiver-operating characteristic
  • Urine samples were collected after digital rectal examination (DRE) of the prostate (DRE urine). This routinely performed examination method allows getting urine samples that contain a certain amount of prostate cells.
  • the DRE urine samples were centrifuged and washed two times using PBS. The resulting cell pellet was resuspended in 700 ⁇ l Qiazol.
  • Total RNA was isolated using the miRNeasy Mini Kit on the QIAcube (all from Qiagen) with manual subsequent DNase I digestion. RNA concentration was determined using a Nanodrop 1000 (Peqlab). RNA integrity was verified on an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, Calif.).
  • cDNA was synthesized from 2 ⁇ 50 ng total RNA using the Superscript III Reverse transcriptase (Applied Biosystems) and random primers according to manufacturer's instructions. Subsequent PCR assays were run using 4 ⁇ l of cDNA. Quantitative real-time PCR was performed using custom and pre-designed TaqMan Gene Expression Assays (Applied Biosystems) for housekeeping (PSA) and target transcripts on an Applied Biosystems 7900HT Real-Time PCR System. All samples were measured in duplicate and the means of these measurements were used for further calculations.
  • RNA sequencing total RNA from 7 DRE urine samples was precipitated using ethanol to concentrate the RNA amount and resuspended in 10 ⁇ l RNase free water.
  • the rRNA removal was performed with 4 ng of total RNA using the Low input Ribo-Zero rRNA Removal Kit (Epicentre, modified by Clontech), resulting in 10 ⁇ l rRNA depleted RNA.
  • Sequencing libraries were prepared from 8 ⁇ l rRNA-depleted RNA using the SMARTER stranded RNAseq Kit (Clontech).
  • the di-tagged cDNA was purified using the Agencourt AMPure XP System Kit (Beckman Coulter).
  • PCR was carried out through 18 cycles to incorporate index barcodes for sample multiplexing and amplify the cDNA libraries.
  • the quality and concentration of the amplified libraries were determined using a DNA High Sensitivity Kit on an Agilent Bioanalyzer (Agilent Technologies). Samples were pooled and cluster generation was performed using 15 pmol/l of the pooled library and the TruSeq PE Cluster Kit v4 (Illumina Inc.) in an Illumina cBOT instrument following the manufacturer's protocol. Sequencing was performed using the HiSeq SBS v4 sequencing reagents (250 cycles) on an Illumina HiSeq2500 sequencing machine (Illumina, Inc.). The details of the sequencing run were as follows: paired-end sequencing strategy; 126 cycles for Read1, 7 cycles for index sequences, and 126 cycles for Read2.
  • PSA prostate specific antigen
  • RNAseq RNA sequencing
  • assays can be set up based on the measurement of these newly discovered biomarkers alone or in combination (or in combination with other markers) in all sources that may contain prostate tumour cells or parts thereof (including vesicles like exosomes, microvesicles, and others as well as free or protein-bound RNA molecules deriving from prostate tumour cells) to be used for the diagnosis of PCa.
  • sources include (but are not limited to) prostate tissue, biopsy material, lymph nodes, urine, ejaculate, blood, blood serum, blood plasma, circulating tumour cells in blood or lymph, as well as any tissue suspected to contain PCa metastases.
  • RNA biomarkers can be done by any method suited to specifically estimate RNA levels, e.g. PCR-based methods like qRT-PCR.
  • the assays can be applied for early diagnosis (screening) of PCa, for predicting the aggressiveness of the tumours (prognosis), and/or for aiding the choice of therapy.
  • FIG. 6 The results from the detection of a selection of biomarkers in urine can be seen in FIG. 6 .
  • the expression levels of all of the biomarkers shown in this figure are higher in the urine of patients suffering from prostate cancer compared to healthy individuals. This shows that analysing the expression level of one of these biomarkers in urine allows diagnosing prostate cancer.
  • Fontenete et al. (Int. braz j urol. vol. 37 no. 6 Rio de Janeiro November/December 2011) showed that the mRNA of PSA is not a suitable biomarker for prostate cancer in urine samples, as it was found to be overexpressed more frequently in healthy patients than in PCa patients in these samples. Therefore, it was not a priori evident that analysing the biomarker expression levels in urine samples could be used to reliably diagnose prostate cancer.

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WO2015082418A1 (en) 2015-06-11
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